Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999984465219685 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM012897)
  • known disease mutation: rs4428 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr9:32974542A>CN/A show variant in all transcripts   IGV
HGNC symbol APTX
Ensembl transcript ID ENST00000436040
Genbank transcript ID N/A
UniProt peptide Q7Z2E3
alteration type single base exchange
alteration region CDS
DNA changes c.561T>G
cDNA.758T>G
g.50625T>G
AA changes C187W Score: 215 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 187
frameshift no
known variant Reference ID: rs121908132
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs4428 (pathogenic for Ataxia-oculomotor apraxia type 1) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM012897)

known disease mutation at this position, please check HGMD for details (HGMD ID CM012897)
known disease mutation at this position, please check HGMD for details (HGMD ID CM012897)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.1410.981
4.4511
(flanking)5.3721
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 18
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      187QDPKMQPCTSSCDQPGF*
mutated  not conserved    187QPCTSSWDQPGF
Ptroglodytes  no alignment  ENSPTRG00000020850  n/a
Mmulatta  no alignment  ENSMMUG00000007724  n/a
Fcatus  no alignment  ENSFCAG00000008728  n/a
Mmusculus  no alignment  ENSMUSG00000028411  n/a
Ggallus  no alignment  ENSGALG00000001954  n/a
Trubripes  no alignment  ENSTRUG00000009794  n/a
Drerio  no alignment  ENSDARG00000027143  n/a
Dmelanogaster  no alignment  FBgn0038704  n/a
Celegans  no homologue    
Xtropicalis  no alignment  ENSXETG00000024143  n/a
protein features
start (aa)end (aa)featuredetails 
182287DOMAINHIT.lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 579 / 579
position (AA) of stopcodon in wt / mu AA sequence 193 / 193
position of stopcodon in wt / mu cDNA 776 / 776
poly(A) signal N/A
conservation
nucleotide level for all changes - no scoring up to now		 N/A
position of start ATG in wt / mu cDNA 198 / 198
chromosome 9
strand -1
last intron/exon boundary 845
theoretical NMD boundary in CDS 597
length of CDS 579
coding sequence (CDS) position 561
cDNA position
(for ins/del: last normal base / first normal base)		 758
gDNA position
(for ins/del: last normal base / first normal base)		 50625
chromosomal position
(for ins/del: last normal base / first normal base)		 32974542
original gDNA sequence snippet TAGCCATGTACATCTTCATGTGATCAGCCAGGATTTTGATT
altered gDNA sequence snippet TAGCCATGTACATCTTCATGGGATCAGCCAGGATTTTGATT
original cDNA sequence snippet CAGCCATGTACATCTTCATGTGATCAGCCAGGATTTTGATT
altered cDNA sequence snippet CAGCCATGTACATCTTCATGGGATCAGCCAGGATTTTGATT
wildtype AA sequence MMRVCWLVRQ DSRHQRIRLP HLEAVVIGRG PETKITDKKC SRQQVQLKAE CNKGYVKVKQ
VGVNPTSIDS VVIGKDQEVK LQPGQVLHMV NELYPYIVEF EEEAKNPGLE THRKRKRSGN
SDSIERDAAQ EAEAGTGLEP GSNSGQCSVP LKKGKDAPIK KESLGHWSQG LKISMQDPKM
QPCTSSCDQP GF*
mutated AA sequence MMRVCWLVRQ DSRHQRIRLP HLEAVVIGRG PETKITDKKC SRQQVQLKAE CNKGYVKVKQ
VGVNPTSIDS VVIGKDQEVK LQPGQVLHMV NELYPYIVEF EEEAKNPGLE THRKRKRSGN
SDSIERDAAQ EAEAGTGLEP GSNSGQCSVP LKKGKDAPIK KESLGHWSQG LKISMQDPKM
QPCTSSWDQP GF*
speed 0.99 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project